On my Droid phone, the salesperson set up my phone using my existing Gmail account. This was supposed to centralize all my email and keep track of everything in one place. Sounds good, but in practice I have not been able to achieve any measure of consistency with my Gmail account.
The problem seems to be that when my Droid samples the Gmail account then the email shows up on the Droid, but then it's status becomes READ and then it does not come to my laptop like I want it to. I have set the email account to Keep EMail on Server and it does stay there, but then the laptop only downloads email whose status is UNREAD. Frustrating. I keep having to resent some emails to myself to get them on my laptop where I really want them.
With my Motorola Droid, my gmail remains in my gmail inbox after my Droid pulls it down and after my laptop pulls it down using Outlook Express. I go out to my gmail account on the internet about once a day or so and delete everything. I also have my Charter email set up to forward a copy to gmail, so I am sure to get it delivered to my Droid, even if I lose my Charter connection for some reason. I don't see any specific settings to make it work this way.
It sounds like the sales person set up the pop3/imap account to access your gmail instead of the actual gmail application...
Does the Icon you use to access your gmail look like a white envelope with a big red "M" coming out of it with the word "GMail" below, or does it appear to be a yellow piece of paper with an "@" sign coming out of it with the word "Mail" below?
If you are using the actual GMail applicatioin, if you read the message on your Android, it will still show up as read on the web site, but it will not dissapear. Also, if you leave it un-read on the phone, it will remain unread on the web site... Read it on the web site, and it will show up read on the phone etc... They are fully synchronized both ways.